Archaeal proviruses TKV4 and MVV extend the PRD1-adenovirus lineage to the phylum Euryarchaeota

Virology

Volumn 375, Issue 1, 2008, Pages 292-300

  Krupovič, Mart ^a,b   Bamford, Dennis H ^a,b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Archaeal viruses; Comparative genomics; PRD1 adenovirus lineage; Virus evolution

Indexed keywords

TRANSFER RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ADENOVIRUS; ARCHAEAL VIRUS; ARTICLE; BACTERIOPHAGE PRD1; BIOINFORMATICS; EURYARCHAEOTA; GENE SEQUENCE; GENOMICS; METHANOCOCCUS VOLTAE; MVV VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLUM; PRIORITY JOURNAL; RNA GENE; SPECIES; THERMOCOCCUS KODAKARAENSIS; TKV4 VIRUS; VIRUS GENOME;

ADENOVIRIDAE; AMINO ACID SEQUENCE; BACTERIOPHAGE PRD1; DNA, ARCHAEAL; DNA, VIRAL; METHANOCOCCUS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROVIRUSES; RNA, TRANSFER; SEQUENCE ALIGNMENT; SULFOLOBUS; THERMOCOCCUS;

ADENOVIRIDAE; ARCHAEA; CRENARCHAEOTA; EUKARYOTA; EURYARCHAEOTA; METHANOCOCCUS VOLTAE; SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS; THERMOCOCCUS KODAKARENSIS;

EID: 42749085392     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2008.01.043     Document Type: Article

References (41)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
2. Bamford D.H. Do viruses form lineages across different domains of life?. Res. Microbiol. 154 (2003) 231-236
3. Bamford D.H., Grimes J.M., and Stuart D.I. What does structure tell us about virus evolution?. Curr. Opin. Struct. Biol. 15 (2005) 655-663
4. Bamford D.H., Ravantti J.J., Rönnholm G., Laurinavičius S., Kukkaro P., Dyall-Smith M., Somerharju P., Kalkkinen N., and Bamford J.K. Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica. J. Virol. 79 (2005) 9097-9107
5. Benson S.D., Bamford J.K., Bamford D.H., and Burnett R.M. Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures. Cell 98 (1999) 825-833
6. Benson S.D., Bamford J.K., Bamford D.H., and Burnett R.M. Does common architecture reveal a viral lineage spanning all three domains of life?. Mol. Cell 16 (2004) 673-685
7. Casjens S. Prophages and bacterial genomics: what have we learned so far?. Mol. Microbiol. 49 (2003) 277-300
8. Espejo R.T., Canelo E.S., and Sinsheimer R.L. Replication of bacteriophage PM2 deoxyribonucleic acid: a closed circular double-stranded molecule. J. Mol. Biol. 56 (1971) 597-621
9. Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., and Imanaka T. Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res. 15 (2005) 352-363
10. Ginalski K., Elofsson A., Fischer D., and Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19 (2003) 1015-1018
11. Hendrix R.W., Smith M.C., Burns R.N., Ford M.E., and Hatfull G.F. Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 2192-2197
12. Humphrey W., Dalke A., and Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 14 (1996) 33-38
13. Hyun J.K., Coulibaly F., Turner A.P., Baker E.N., Mercer A.A., and Mitra A.K. The structure of a putative scaffolding protein of immature poxvirus particles as determined by electron microscopy suggests similarity with capsid proteins of large icosahedral DNA viruses. J. Virol. 81 (2007) 11075-11083
14. Ilyina T.V., and Koonin E.V. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res. 20 (1992) 3279-3285
15. Khayat R., Tang L., Larson E.T., Lawrence C.M., Young M., and Johnson J.E. Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 18944-18949
16. Kraft P., Oeckinghaus A., Kümmel D., Gauss G.H., Gilmore J., Wiedenheft B., Young M., and Lawrence C.M. Crystal structure of F-93 from Sulfolobus spindle-shaped virus 1, a winged-helix DNA binding protein. J. Virol. 78 (2004) 11544-11550
17. Krupovič M., and Bamford D.H. Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria. BMC Genomics 8 (2007) 236
18. Laurinmaki P.A., Huiskonen J.T., Bamford D.H., and Butcher S.J. Membrane proteins modulate the bilayer curvature in the bacterial virus Bam35. Structure 13 (2005) 1819-1828
19. Lovell S.C., Davis I.W., Arendall III W.B., de Bakker P.I., Word J.M., Prisant M.G., Richardson J.S., and Richardson D.C. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 50 (2003) 437-450
20. Maaty W.S., Ortmann A.C., Dlakić M., Schulstad K., Hilmer J.K., Liepold L., Weidenheft B., Khayat R., Douglas T., Young M.J., and Bothner B. Characterization of the archaeal thermophile Sulfolobus turreted icosahedral virus validates an evolutionary link among double-stranded DNA viruses from all domains of life. J. Virol. 80 (2006) 7625-7635
21. Maiorano D., Lutzmann M., and Méchali M. MCM proteins and DNA replication. Curr. Opin. Cell Biol. 18 (2006) 130-136
22. Makino S., Amano N., Koike H., and Suzuki M. Prophages inserted in archaebacterial genomes. Proc. Jpn. Acad., Ser. B 75 (1999) 166-171
23. Männistö R.H., Kivelä H.M., Paulin L., Bamford D.H., and Bamford J.K. The complete genome sequence of PM2, the first lipid-containing bacterial virus to be isolated. Virology 262 (1999) 355-363
24. Marti-Renom M.A., Stuart A.C., Fiser A., Sanchez R., Melo F., and Sali A. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29 (2000) 291-325
25. McGeoch A.T., and Bell S.D. Eukaryotic/archaeal primase and MCM proteins encoded in a bacteriophage genome. Cell 120 (2005) 167-168
26. Morikawa M., Izawa Y., Rashid N., Hoaki T., and Imanaka T. Purification and characterization of a thermostable thiol protease from a newly isolated hyperthermophilic Pyrococcus sp. Appl. Environ. Microbiol. 60 (1994) 4559-4566
27. Nandhagopal N., Simpson A.A., Gurnon J.R., Yan X., Baker T.S., Graves M.V., Van Etten J.L., and Rossmann M.G. The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 14758-14763
28. Porter K., Kukkaro P., Bamford J.K., Bath C., Kivelä H.M., Dyall-Smith M.L., and Bamford D.H. SH1: a novel, spherical halovirus isolated from an Australian hypersaline lake. Virology 335 (2005) 22-33
29. Prangishvili D., Garrett R.A., and Koonin E.V. Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res. 117 (2006) 52-67
30. Reiter W.D., Palm P., and Yeats S. Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res. 17 (1989) 1907-1914
31. Rice G., Tang L., Stedman K., Roberto F., Spuhler J., Gillitzer E., Johnson J.E., Douglas T., and Young M. The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 7716-7720
32. Russell R.B., and Barton G.J. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 14 (1992) 309-323
33. She Q., Shen B., and Chen L. Archaeal integrases and mechanisms of gene capture. Biochem. Soc. Trans. 32 (2004) 222-226
34. Strömsten N.J., Bamford D.H., and Bamford J.K. In vitro DNA packaging of PRD1: a common mechanism for internal-membrane viruses. J. Mol. Biol. 348 (2005) 617-629
35. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
36. Verheust C., Fornelos N., and Mahillon J. GIL16, a new Gram-positive tectiviral phage related to the Bacillus thuringiensis GIL01 and the Bacillus cereus pBClin15 elements. J. Bacteriol. 187 (2005) 1966-1973
37. Vestergaard G., Häring M., Peng X., Rachel R., Garrett R.A., and Prangishvili D. A novel rudivirus, ARV1, of the hyperthermophilic archaeal genus Acidianus. Virology 336 (2005) 83-92
38. Whitman W.B., Shieh J., Sohn S., Caras D.S., and Premachandran U. Isolation and characterization of 22 mesophilic methanococci. Syst. Appl. Microbiol. 7 (1986) 235-240
39. Woese C.R., Kandler O., and Wheelis M.L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. U. S. A. 87 (1990) 4576-4579
40. Wood A.G., Whitman W.B., and Konisky J. Isolation and characterization of an archaebacterial viruslike particle from Methanococcus voltae A3. J. Bacteriol. 171 (1989) 93-98
41. Yan X., Chipman P.R., Castberg T., Bratbak G., and Baker T.S. The marine algal virus PpV01 has an icosahedral capsid with T = 219 quasisymmetry. J. Virol. 79 (2005) 9236-9243